Freesurfer October 2021

freesurfer@nmr.mgh.harvard.edu

81 participants
113 discussions

Confusion about discrete variable in the FSGD file
by Thalhammer, Melissa 08 Nov '21

08 Nov '21

External Email - Use Caution Dear FreeSurfer users, I am interested in cortical thickness differences between preterm (PT) and fullterm (FT) individuals. I have used DODS with mri_glmfit and wanted to regress out scanner (4 sites) and sex in the analysis, using the attached FSGD file. Both of the variables are discrete and I have found different information on how to include discrete variables into the model. I have followed Andrew Jahn's blog at first who includes discrete variables in the variable list just as continuous ones and specifies them with values of 0 or 1 (https://secure-web.cisco.com/1mCX947TtGflWAdnM3CtHlWXx5Aa4vkeu9B25dEdIVjquj…) I have adapted this procedure and have specified my gender values as 1 and 2 (simply because it was stated like this in the participants information sheet I have received). Recently, I have read a post on the mail archive, where Doug states: "you should not code gender and handedness as a continuous variables. In doing this, you are saying that you expect right handers to have 2x the thickness as left handers (or females to have 2x the thickness as males)" (https://secure-web.cisco.com/1A4RpPVoEFVSno401uhBm0BawiKw27S9-5VpEg7YyqN3rI…) When following this argument, this would also hold for continuous variables, i.e., a patient aged 50 would have 2x the thickness of a patient aged 25. So my question is how to correctly deal with discrete variables and why you have suggested to code gender as classes instead of variables. What is the actual difference? How does the model treat classes and variables? Cheers and many thanks in advance, Melissa Thalhammer

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adding covariates to a longitudinal glmfit model
by Zeng, Qi 08 Nov '21

08 Nov '21

External Email - Use Caution Hi Experts, After completing long_mris_slopes to get the rate of change and then concatenating them into one.mgh file for group analysis (mris_preproc). I am finally getting to mris_glmfit. Got a couple of questions along the way. 1). if I conducted long_mris_slopes, and got for example, lh.long.thickness-rate.fwhm10.fsaverage.mgh. Do I need to do a surface smoothing again (mri_surf2surf) before mris_glmfit? 2). I construct covariates in FSGD besides the group contrast that I am interested in. How do I add covariates into the glmfit model to control for the covariates as I contrast groups in terms of the rate of changing (CV vs. NCV groups) . Do I add them into --C as (1, -1, 0(age), 0(gender), 0(race)). mri_glmfit --y {$hemi}.{$meas}-rate.{$smoothness}.mgh --fsgd FSGD/{$study}.fsgd doss --C Contrasts/CV-NCV.mtx (1, -1) --C Contrasts/NCV-CV.mtx (-1, 1) --surf fsaverage {$hemi} --cortex --glmdir {$hemi}.{$meas}-rate.{$study}.{$smoothness}.glmdir Best, Zeno --

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Total volumes SAMSEG
by Nederpelt, D.R. van (David) 02 Nov '21

02 Nov '21

External Email - Use Caution Dear SAMSEG developers, Is there an easy way/specific function to compute the total volumes (GM, WM and Total Brain) after the cross sectional processing pipeline has been run? I currently add the volumes specified here: MorphometryStats - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1TiZSqlkmJdSG6YomLyN1O5wCUsd9cdQzzIoKCQYS9Wpvi…> However, adding the WM volumes (lhCerebralWhiteMatter + rhCerebralWhiteMatter + WM hypointensities) results in lower volumesthan the volumes found with FreeSurfer. Thank you very much in advance! Best regards, David [cid:image002.png@01D40E30.3E299A80] David van Nederpelt, MSc. | PhD Candidate Radiology and Nuclear Medicine Amsterdam UMC, Location VUmc | PK -1 X 004 | De Boelelaan 1118, 1081 HZ Amsterdam, the Netherlands T: +31 20 444 6480 | E: d.vannederpelt(a)amsterdamumc.nl<mailto:d.vannederpelt@amsterdamumc.nl> http://secure-web.cisco.com/1EOtsCiWTwBLCVMkC2cEggLJndUZQC9bJDTTa84lDglqlKV…<http://secure-web.cisco.com/1adKHUXOwhS5An078rgDU8DhS5pGcVaF-bemoEwstJMOWdV…> | http://secure-web.cisco.com/1MykofUmqPylr7OSHojIjyyuz3FqKchVPIVM4VJj6JPJzvT…<http://secure-web.cisco.com/1gpC425-YWhlfpRlTm0wPHu3H0yqPdczn6ZxyBZtVEFl5eb…> / http://secure-web.cisco.com/1IDr1ToLQ00j-N7JGdkZizZ2EY4BfRaX-Ni0bhB33BkT_pJ…<http://secure-web.cisco.com/1wXJqt2HAZw1ZuD0nu0MtMhTFzaeK7O7CKFnLDqQmLsmS7l…> ______________________________________________________ ______________________________________________________ VUmc disclaimer : http://secure-web.cisco.com/13cespwJDanP8jSeJT-F5DbVhbpJ9dqA3oMmUiNIdESzfsi… AMC disclaimer : http://secure-web.cisco.com/1-TwAPrU-0Wch-3LbY82fTZ4s74MTy5spCul9ZUUp4f7Au_…

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Inflated surfaces on FS7 looking different
by DIANA ORTEGA CRUZ 02 Nov '21

02 Nov '21

External Email - Use Caution Dear FreeSurfer team, I am experiencing a display problem in the FreeView version of FreeSurfer 7 for inflated surfaces. The inflated surfaces from my fsaverage folder look as in the screenshot attached, missing the gyri and sulci coloring and having a see-through pattern. My FreeView version is 3.0 Build Jul 23 2020. One of my colleagues tested opening inflated surfaces using different versions of FreeView, and these also look see-through using a version from FS7, but not using a version from FS6. Have any of you encountered a similar display for inflated surfaces? Do you know if this could be changed? Any advice would be much appreciated!! Thanks a lot. Best, Diana Ortega Cruz. PhD Student Laboratory for Clinical Neuroscience Centro de Tecnología Biomédica - Universidad Politécnica de Madrid

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Re: [Freesurfer] Base correction, longitudinal analysis
by Eszter Boros 01 Nov '21

01 Nov '21

External Email - Use Caution Thank you for your answer! I think I should clarify this question a little bit. So this is about correcting the Base. And run recon-all *after *correcting the Base. What command should I use here? if I want to regenerate only the Base after correcting it? Because the common below does not work: (ERROR: must specify subjects for base subject using -base-tp) recon-all -base OAS2_0057 -autorecon-pial But if I use "recon-all -base OAS2_0001 -tp OAS2_0001_MR1 -tp OAS2_0001_MR2 -all" that just creates a new Base based on the cross MR1 and MR2. My question is how can I regenerate the corrected Base? What command should I use? Thank you so much! All the best, Eszter Boros Eszter Boros <boros.eszter0226(a)gmail.com> ezt írta (időpont: 2021. aug. 8., V, 19:04): > Dear FreeSurfer Team, > > I am working on a longitudinal pipeline and after correcting the Cross and > generating the Base, I can still see some pial problems sometimes (on the > Base). > > I read on the Freesurfer website that it is possible to correct and > regenerate only the Base, but when I use this command: > > recon-all -base OAS2_0057 -autorecon-pial > > /where OAS2_0057 is the name of the Base/ > > I get the following error message: > > ERROR: must specify subjects for base subject using -base-tp > > > Why is this not working? I am using Freesurefer 7.1.1. > > Thank you so much! > > All the best, > Eszter Boros > >

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Registering DTI fiber tracts (from MRtrix3) to FreeSurfer registered surfaces.
by Sherin Sugathan 31 Oct '21

31 Oct '21

External Email - Use Caution Hi!!, I have a two time point brain dataset of a single patient. The data consists of structural and DTI for both timesteps. I run FreeSurfer on each timestep separately for generating brain surfaces. When I display the brain surfaces(from both timesteps) together, they were appearing unregistered. Then I figured out that I need to use*FreeSurfer Longitudinal*to fix the registration problem. If I use FreeSurfer longitudinal, then it will most likely register both time point data to a common template, and my registration problem will be solved. I also want to display fiber tracts generated from MRtrix3 along with the brain surfaces generated by FreeSurfer. The problem is that the DTI data will not be touched by FreeSurfer. I am anticipating that this will become a problem to display fibertracts and brain surface properly. Please see below table that shows the data discrepancy I am expecting: |+----------------------------------+-----------------------------------+ | time t0 | time t1 | +----------------------------------+-----------------------------------+ | T1.nii(registered by FreeSurfer) | T1.nii (registered by FreeSurfer) | | DTI.nii (unregistered DTI image) | DTI.nii (unregistered DTI image) | +----------------------------------+-----------------------------------+ | FreeSurfer only takes in the structural data for brain surface generation and it leaves the DTI image untouched. Later, the fiber tracts generated using MRtrix3 won’t align with the FreeSurfer surfaces. How can fix this problem? Do you think it is possible to fetch some transformation and apply to DTI fiber tracts to fix the issue? Thanks in advance Reshma

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Magnetization Transfer Images and recon-all
by Marlene Tahedl 31 Oct '21

31 Oct '21

External Email - Use Caution Hi! I have a couple of Magnetization Transfer MR images from a group of patients which I would like to analyze using the FreeSurfer pipeline. However, when applying "recon-all" to those images, the algorithm stops after just a few minutes. Although it says "finished without error", no images have been produced. Is there a way to apply recon-all to MT, maybe some conversion to make the MT images look more like a T1? Thanks! Marlene.

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Re: [Freesurfer] A question regarding a Freeview command
by Douglas N. Greve 31 Oct '21

31 Oct '21

I don't think there is anything specific for the --table option, but everything else is the same. On 10/24/2021 4:31 PM, Alvarado,Luis R wrote: > > External Email - Use Caution > > Hi Douglas, > > I was wondering if there are any “--table option” specific tutorial > for the mri_glmfit function. I am trying to decide wheatear to export > my ROI results to R or use the mri_glmfit function. > > Best, > > Luis >

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results visualization
by Marina Fernández 29 Oct '21

29 Oct '21

External Email - Use Caution Dear experts, Do you know what are the steps to follow to visualize a surface-map of freesurfer results in Caret? Thank you very much in advance. Best regards, Marina

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Re: [Freesurfer] developer password
by fsbuild 29 Oct '21

29 Oct '21

External Email - Use Caution Sure - sending password and upgrade instructions to your private email shortly. - R. On Oct 29, 2021, at 13:55, Eli Bulger <esbulger(a)cmu.edu> wrote:        External Email - Use Caution        Hello,I am hoping to use Freesurfer on Windows 10. I have tried to use VirtualBox, but it requires a developer password. I have seen many emails on this mailing list where the password is provided through email. Is it possible to have a copy sent to this email? Thank you,_______________________Eli BulgerPh.D. Student, Biomedical EngineeringCarnegie Mellon University_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer October 2021